When you have bit of information in your mind (like you mentioned) it's best to jot them down. This way after you have all the information you need you can organize that information.
I find that if I try to focus my thoughts at this point I tend to lose some of the bits and pieces.
Organizing my writing all depends on what I am writing. If I am working on a novel this is my sequence:
- jot down my concept/idea
- work out the plot
- create the characters
- outline each chapter
- build each chapter
For articles I outline the different points which I want to put across to my readers using the basic: why, what, how, where, when. For example:-
-answering the question of "what is?"
-elaborating on why it is
-expanding on how it is